Where does Minecraft store scoreboard objectives?
The game stores the scoreboard data of a world into the scoreboard.dat file in the save folder of that world (as shown on the wiki: https://minecraft.gamepedia.com/Scoreboard#NBT_format).
I tried this myself by shutting down the server, deleting the file and activating the server again. The objective was removed once I did this, which makes me think your server was still running when you deleted the file. If that's the case, you need to shut the server down so that the objectives don't stay loaded in memory otherwise, the server will write them to the file again.